Hi all, Can someone tell me where in the AutoBuild GUI I can set "phases_from_resolve"? I've looked for it in the "set variable" section, but it's not listed. Thanks!
Hi Mo, There isn't any place in the AutoBuild GUI specifically for "phases_from_resolve". If you really want to set this parameter you can go to the "uncommon inputs" window and set "resolve_command" to "phases_from_resolve". I think that you don't want to do this, however. I am assuming that this means that you are using a density-modified map as input to AutoBuild with data=my_density_modified_map.mtz. What you want to do instead is say (or set in the GUI): data=my_experimental_fobs_and_phases.mtz \ input_map_file=my_density_modified_map.mtz and then AutoBuild will start from your density modified map, but it will use experimental phase information as the prior phase information. It will also automatically set the parameter "phases_from_resolve" so that that you do not have to. I hope that helps! -Tom T Hi all, Can someone tell me where in the AutoBuild GUI I can set "phases_from_resolve"? I've looked for it in the "set variable" section, but it's not listed. Thanks! _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Thanks for the e-mail!
I think I've figured out the problem. I had been using the GUI to set
"input_map_file" and "input_map_labels" rather than using "Optional map
coefficient file name". It wasn't reading in the solvent flattened data
correctly (and thus not setting "phases_from_resolve").
In addition there seems to be a bug in how the optional map file labels are
read, since:
temporary.com:LABIN FP=PHIdm PHIB=FOMdm FOM=Fdm
Is there a fix for this (version 1.3), as I've flipped them round and still
get them mis-assigned?
Cheers!
On Fri, Feb 27, 2009 at 7:49 PM, Thomas C. Terwilliger wrote: Hi Mo, There isn't any place in the AutoBuild GUI specifically for
"phases_from_resolve". If you really want to set this parameter you can
go to the "uncommon inputs" window and set "resolve_command" to
"phases_from_resolve". I think that you don't want to do this, however. I am assuming that this
means that you are using a density-modified map as input to AutoBuild with
data=my_density_modified_map.mtz. What you want to do instead is say (or set in the GUI): data=my_experimental_fobs_and_phases.mtz \
input_map_file=my_density_modified_map.mtz and then AutoBuild will start from your density modified map, but it will
use experimental phase information as the prior phase information. It will
also automatically set the parameter "phases_from_resolve" so that that
you do not have to. I hope that helps!
-Tom T Hi all, Can someone tell me where in the AutoBuild GUI I can set
"phases_from_resolve"? I've looked for it in the "set variable" section,
but
it's not listed. Thanks!
_______________________________________________
phenixbb mailing list
[email protected]
http://www.phenix-online.org/mailman/listinfo/phenixbb _______________________________________________
phenixbb mailing list
[email protected]
http://www.phenix-online.org/mailman/listinfo/phenixbb
Hi Mo,
Yes, you're right you want to use "Optional map coefficient file name" to
input your density-modified phases. I'm sorry about the bug in reading
the labels. I think that if you download the current development version
from the website at www.phenix-online.org then this will go away. (If not,
please let me know!)
Also note that the temporary.com file running density modification won't
actually say "phases_from_resolve". It should however say
"hklstart"....something.mtz which sets that flag inside resolve.
All the best,
Tom T
--------------------
Thanks for the e-mail!
I think I've figured out the problem. I had been using the GUI to set
"input_map_file" and "input_map_labels" rather than using "Optional map
coefficient file name". It wasn't reading in the solvent flattened data
correctly (and thus not setting "phases_from_resolve").
In addition there seems to be a bug in how the optional map file labels
are
read, since:
temporary.com:LABIN FP=PHIdm PHIB=FOMdm FOM=Fdm
Is there a fix for this (version 1.3), as I've flipped them round and
still
get them mis-assigned?
Cheers!
On Fri, Feb 27, 2009 at 7:49 PM, Thomas C. Terwilliger
wrote: Hi Mo, There isn't any place in the AutoBuild GUI specifically for
"phases_from_resolve". If you really want to set this parameter you can
go to the "uncommon inputs" window and set "resolve_command" to
"phases_from_resolve". I think that you don't want to do this, however. I am assuming that
this
means that you are using a density-modified map as input to AutoBuild
with
data=my_density_modified_map.mtz. What you want to do instead is say (or set in the GUI): data=my_experimental_fobs_and_phases.mtz \
input_map_file=my_density_modified_map.mtz and then AutoBuild will start from your density modified map, but it
will
use experimental phase information as the prior phase information. It
will
also automatically set the parameter "phases_from_resolve" so that that
you do not have to. I hope that helps!
-Tom T Hi all, Can someone tell me where in the AutoBuild GUI I can set
"phases_from_resolve"? I've looked for it in the "set variable" section,
but
it's not listed. Thanks!
_______________________________________________
phenixbb mailing list
[email protected]
http://www.phenix-online.org/mailman/listinfo/phenixbb _______________________________________________
phenixbb mailing list
[email protected]
http://www.phenix-online.org/mailman/listinfo/phenixbb
participants (2)
-
Mo Wong -
Thomas C. Terwilliger